Kennedy was named manager in May, signing a two-year contract with Swindon.
But he has now been shown the door after just two league wins this season and six losses in 13 games, with the club 22nd on the table.
A club statement read: "Swindon Town Football Club have parted company with head coach Mark Kennedy.
"Marcus Bignot, Steve Mildenhall and Gavin Gunning will continue in their current positions, with all three first-team coaches in place to oversee this weekend's game against Gillingham.
"Everyone at Swindon Town Football Club would like to express their appreciation to Mark for his commitment and hard work during his time with the Club and wish him all the best in the future.
"A further update on the club's new head coach will be provided at the earliest opportunity."